Is CD93 p.Val117Gly (c.350T>G) pathogenic?

CD93 p.Val117Gly (c.350T>G) is classified Benign in CD93 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-06-02). AlphaMissense: likely benign (0.2732); Common (popmax 33.7%, sas) — too common for a highly-penetrant pathogenic allele; Associated with CD93-related disorder.

What condition is associated with CD93 p.Val117Gly (c.350T>G)?

CD93 p.Val117Gly (c.350T>G) is associated with CD93-related disorder (ClinVar).

What do computational predictors say about CD93 p.Val117Gly (c.350T>G)?

AlphaMissense predicts likely benign (score 0.2732) — an in-silico prediction, not a clinical call.

CD93 p.Val117Gly

Q: How common is CD93 p.Val117Gly (c.350T>G) in the general population?

CD93 p.Val117Gly (c.350T>G) is common (popmax 33.7%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.350T>G · rs781389958 · VCV3034758

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2732 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 33.7%, sas) — too common for a highly-penetrant pathogenic allele

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CD93-related disorder

Computational evidence

Protein change
AlphaMissense	0.2732	likely benign
REVEL	0.66	pathogenic-leaning
SaProt	LLR -9.38	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.3	GERP 0.81, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 2,239 bp · p 0.011 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 33.7% South Asian · 17,294/51,318 alleles

Filtering AF 33.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 33.1%

Overall 22.1% 84,031/380,212 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	34%	3
South Asiangrpmax	33.7%	3
Admixed American	26.8%	4
Remaining individualsnot grpmax-eligible	25.6%	4
Ashkenazi Jewishnot grpmax-eligible	25.5%	4
African / African-American	22.3%	4
Finnishnot grpmax-eligible	20.2%	5
European (non-Finnish)	18.9%	5
East Asian	17.9%	6
Middle Eastern	13.1%	8

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CD93
Protein: p.Val117Gly
Coding: c.350T>G
MANE Select: NM_012072
dbSNP: rs781389958
Type: single nucleotide variant
Location: chr20:23085843 (GRCh38)
Gene constraint: LOEUF 1.237 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.07 · 2 PDB
Residue 117: the c-type lectin domain

Full CD93 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD93-related disorder

Similar variants

CD93 p.Arg634Ter Uncertain significance ★ same condition
CD93 p.Met187Ile Uncertain significance ⚠ same condition
CD93 p.Arg496Cys Likely benign ⚠ same condition
CD93 p.Arg496His Likely benign same condition
CD93 p.Ser41= Likely benign same condition
CD93 p.Glu484del Likely benign same condition
CD93 p.Arg496= Benign/Likely benign ★★ same type
CD93 p.Gly448= Benign ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cd93-p-val117gly (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown